LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies

variable    r     index 4
variable    steps index 100000
variable    T     index 0.5
variable    P     index 0.1
variable    seed  index 980411

units       lj
dimension   2

atom_style  body rounded/polygon 1 6
atom_modify map array
read_data   data.squares
  orthogonal box = (0 0 -0.5) to (12 12 0.5)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies

replicate   $r $r 1
replicate   4 $r 1
replicate   4 4 1
  orthogonal box = (0 0 -0.5) to (48 48 0.5)
  2 by 2 by 1 MPI processor grid
  32 atoms
  Time spent = 0.000329733 secs

velocity    all create $T ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 980411 dist gaussian mom yes rot yes

change_box  all boundary p f p

variable cut_inner  equal 0.5
variable k_n        equal 100
variable k_na       equal 2
variable c_n        equal 0.1
variable c_t        equal 0.1
variable mu         equal 0.1
variable delta_ua   equal 0.5

pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2

comm_modify vel yes

neighbor     0.5 bin
neigh_modify every 1 delay 0 check yes

timestep     0.001

#fix         1 all nve/body
#fix         1 all nvt/body temp $T $T 1.0
fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0

fix          2 all enforce2d
fix          3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0

#compute      1 all body/local id 1 2 3
#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]

thermo_style custom step ke pe etotal press
thermo       1000

#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
#dump_modify  2 pad 6

run          ${steps}
run          100000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.15685
  ghost atom cutoff = 6.15685
  binsize = 3.07843, bins = 16 16 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair body/rounded/polygon, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes
Step KinEng PotEng TotEng Press 
       0     0.484375         0.25     0.734375 0.0067274306 
    1000   0.51467204 0.00099202506   0.51566407  0.013452386 
    2000   0.55674899 0.0040762275   0.56082522 0.0034529066 
    3000    0.7546177   0.02259362   0.77721132  0.003650781 
    4000   0.72710218   0.10284108   0.82994326 0.0059629371 
    5000   0.57710119  0.069052154   0.64615335 0.00053937664 
    6000   0.53848104  0.041891152   0.58037219 0.0018693259 
    7000   0.61777485  0.033380825   0.65115568 0.0027584782 
    8000   0.47427732  0.059553658   0.53383098  0.017087698 
    9000   0.46820943  0.064379697   0.53258913   0.02325702 
   10000   0.46605511   0.02332689     0.489382  0.013699209 
   11000   0.57547516  0.090133398   0.66560855 0.0083913962 
   12000     0.465348  0.084853345   0.55020135  0.006231552 
   13000   0.55340889   0.07116165   0.62457054  0.030622563 
   14000   0.58866362  0.052281859   0.64094548 0.0079106838 
   15000   0.51757672   0.12255618    0.6401329  0.014005369 
   16000   0.42696011  0.086987541   0.51394765 -0.0017128649 
   17000   0.37612579   0.13054778   0.50667357 0.0046284992 
   18000   0.47659682   0.14670523   0.62330205   0.02206928 
   19000   0.47897909   0.15540332   0.63438241   0.02544138 
   20000   0.59377323   0.15357757    0.7473508  0.030262926 
   21000   0.52781204   0.22074491   0.74855695 -0.0022170167 
   22000   0.44843285   0.12779345    0.5762263 0.0097268482 
   23000   0.60400735   0.18098124   0.78498858   0.05778325 
   24000   0.58254338    0.1570243   0.73956769  0.022530491 
   25000   0.60524318   0.23660272    0.8418459  0.062530421 
   26000   0.45892702   0.34294121   0.80186823  0.038657393 
   27000   0.58418023   0.19551937    0.7796996 -0.0055396645 
   28000   0.45655369   0.26718934   0.72374303  0.006593108 
   29000   0.50277299    0.1747088   0.67748179  0.016059369 
   30000   0.38640717    0.1631573   0.54956447  0.036055723 
   31000   0.46944541   0.22076826   0.69021367  0.014334038 
   32000   0.53862858   0.26867594   0.80730452  0.057406282 
   33000   0.45666352   0.21796554   0.67462906  0.056555205 
   34000   0.51644038   0.21866786   0.73510824     0.015713 
   35000   0.50489584    0.1596236   0.66451945  0.040400644 
   36000   0.41723489   0.16227853   0.57951342   0.02863261 
   37000     0.481638   0.28830624   0.76994424  0.038381986 
   38000    0.6036094   0.33479287   0.93840227 0.0032059452 
   39000   0.47822122   0.18876355   0.66698476  0.029252649 
   40000   0.54949607   0.35011086   0.89960693  0.093909148 
   41000   0.54876522   0.27501735   0.82378257 -0.0084167014 
   42000   0.67801592   0.18102522   0.85904114 -0.0058395209 
   43000   0.54342066   0.34322081   0.88664146   0.12263806 
   44000   0.46672513   0.29749157   0.76421671  0.051073701 
   45000    0.4679867   0.25820875   0.72619545  0.069790993 
   46000   0.59598501   0.22285276   0.81883777  0.050578807 
   47000   0.48858341   0.29811577   0.78669917  0.080971431 
   48000   0.41238073   0.29362937    0.7060101  0.031893588 
   49000   0.61516435   0.33082609   0.94599044 -0.010710982 
   50000   0.57576635   0.37137185   0.94713819  0.062160249 
   51000   0.54614001   0.36960628   0.91574629 -0.0083424769 
   52000   0.42232354   0.25214442   0.67446796  0.028666126 
   53000   0.43025129   0.24479385   0.67504514  0.030342054 
   54000   0.54614922   0.29602426   0.84217348  0.083070642 
   55000   0.60719748    0.3577285   0.96492598  0.053799744 
   56000   0.47073149   0.31070429   0.78143579  0.083895368 
   57000   0.56861582   0.33249784   0.90111366  0.032324233 
   58000   0.75061035   0.33313728    1.0837476  0.031039937 
   59000   0.59473893   0.48870773    1.0834467  0.039503585 
   60000   0.55252481   0.38350562   0.93603043 0.0027643882 
   61000   0.45010855   0.43945065    0.8895592  0.028168222 
   62000   0.63942467   0.53372899    1.1731537   0.13790959 
   63000   0.69407873   0.37980402    1.0738828  0.035919608 
   64000   0.54898275   0.39910419   0.94808693 0.0015016851 
   65000   0.58229838   0.42300361     1.005302  0.089787193 
   66000   0.53443537    0.5597136     1.094149 -0.015781756 
   67000   0.59212426   0.56172146    1.1538457  0.030464683 
   68000   0.68164926   0.48724393    1.1688932  0.071465948 
   69000   0.59721737   0.49476309    1.0919805   0.07575647 
   70000   0.52314551   0.31950477   0.84265028   0.11206672 
   71000   0.53230509   0.53846575    1.0707708 0.0047204701 
   72000   0.71341933    0.4924749    1.2058942     0.116568 
   73000   0.70498496   0.54121008     1.246195   0.11210249 
   74000   0.54188682   0.61729607    1.1591829  0.044083048 
   75000   0.44073609   0.42072284   0.86145893 -0.041508511 
   76000   0.51225567   0.36848317   0.88073884 -0.028636748 
   77000    0.6517329    0.5503086    1.2020415  0.049605026 
   78000   0.60053898   0.52760266    1.1281416  0.094361256 
   79000   0.51560788   0.46563043   0.98123832  -0.03336136 
   80000   0.53357884   0.60743981    1.1410186  0.027259883 
   81000    0.6256228   0.40412923     1.029752  0.083274981 
   82000    0.6903519   0.69599412     1.386346     0.168747 
   83000   0.62621394   0.50082841    1.1270424   0.12294403 
   84000    0.5682146   0.73827702    1.3064916  0.085884707 
   85000   0.48179077   0.73669563    1.2184864  0.065002035 
   86000   0.61101399   0.80673836    1.4177523  0.037555163 
   87000   0.52278725   0.71608722    1.2388745  0.020943688 
   88000   0.53318823   0.50916748    1.0423557  -0.01946691 
   89000   0.56428713   0.56042234    1.1247095  0.040998134 
   90000   0.58720508   0.66023073    1.2474358  0.040313529 
   91000   0.61509407   0.86254343    1.4776375   0.15215034 
   92000    0.5640475   0.57694543    1.1409929   0.10238679 
   93000   0.60586378   0.67978456    1.2856483 -0.043948113 
   94000   0.75406595   0.74795347    1.5020194  0.015341415 
   95000    0.4974314   0.60192267    1.0993541 -0.018173218 
   96000   0.50048302   0.82845218    1.3289352  0.045394283 
   97000   0.65335222    0.6470855    1.3004377  0.011624967 
   98000   0.65693072   0.45222133     1.109152   0.13763684 
   99000   0.60573344   0.50284289    1.1085763   0.12853674 
  100000   0.50677068   0.58143063    1.0882013   0.11351254 
Loop time of 3.24642 on 4 procs for 100000 steps with 32 atoms

Performance: 2661396.711 tau/day, 30803.203 timesteps/s
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.64148    | 0.70244    | 0.76391    |   6.5 | 21.64
Neigh   | 0.0049012  | 0.0050417  | 0.0052478  |   0.2 |  0.16
Comm    | 0.79447    | 0.88412    | 0.97443    |   8.1 | 27.23
Output  | 0.001776   | 0.0031438  | 0.0072262  |   4.2 |  0.10
Modify  | 1.325      | 1.3684     | 1.4049     |   2.4 | 42.15
Other   |            | 0.2833     |            |       |  8.73

Nlocal:    8 ave 9 max 7 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost:    14 ave 15 max 13 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs:    13.25 ave 16 max 11 min
Histogram: 1 0 1 0 0 0 1 0 0 1

Total # of neighbors = 53
Ave neighs/atom = 1.65625
Neighbor list builds = 2654
Dangerous builds = 0
Total wall time: 0:00:03
